Jessica Nasica
Universit é de Montréal
Montr éal, Québec, Canada

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Overview of the simulation method
Why use “simulator”?
The OPEP force-field
Running the simulation: what you need to get started
The simulation step by step
The output of the “simulator”
The analysis tools
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The PTWHAM analysis
The RMSD analysis
Secondary structure tools
Contacts tools
Clustering tools
Graphical tools and various useful scripts

 REMD simulation ( Replica Exchange
Molecular Dynamics )
 A simplified coarse-grained potential: OPEP

 It can be used:
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To study aggregation processes
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To check for the stability of a particular molecular assembly
 The simplified force-field allows to reach bigger time scales more efficiently:
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To study long-range proteins motions
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To extract accurate thermodynamics properties
P. Derreumaux, N. Mousseau – J. Chem. Phys. 126 , 025101 (2007)

OPEP = Optimized Potential for
Efficient structure Prediction
 Reduced-protein model:
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A 6-particle model with a detailed representation of the backbone (except for
Proline)
Each side chain is represented as one particle and defined by one centroid
Implicit solvent  solvent effects included in the interaction parameters
Maupetit et al.
- Proteins 2007; 69 :394-408
/
Chebaro et al.
– J. Phys. Chem. B 2008

 OPEP energy function:
E

E local
 Local Forces:
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E nonbonded
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E
H
 bond
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Includes changes in bond lengths and valence angles for all particles and changes in improper torsions of the side chains.
Nonbonded Forces:
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Van der Waals , electric and hydrophobic forces  short- and longrange interactions are computed separately.
Use of a pairwise contact potential between side chains represented either by a 12-6 potential or by a 6-potential.
Hydrogen-bonding Forces:
2 terms  2-body H-bonds
 4-body effects = cooperative energies between H-bonds
Maupetit et al.
- Proteins 2007; 69 :394-408
/
Chebaro et al.
– J. Phys. Chem. B 2008

 What you need to get started:
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The executable file after compilation of the code
The parameter file ‘simulator.sh’
Your ‘.pdb’ file in an OPEP format
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The corresponding topology file (.top), residue description file (.list) and ‘ichain.dat’ file
The ‘cutoff.dat’ and ‘scale.dat’ files
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A link file and a qsub script

 Step 1:Minimization: finding a stable starting point
It makes sure that the structure’s energy is minimized using ART.
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F on _ each _ atom
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0
The 2 phases of ART:
-Activation phase  the structure is pushed towards a saddle point
-Relaxation phase  the structure is pushed slightly over the saddle point and relaxed to a new local energy minimum
Mousseau et al.
– Frontiers in Bioscience 13 - 2008; 4495-4516

 Step 1:Minimization: the output
The minimized configuration is written in the file “relaxed_conformation.pdb”.
The data resulting from each minimization step is written in “log.file”:
Total Energy .
towards a minimum
Net Force to 0
Decrease in potential energy term
Velocity Rmsd value
Decrease in kinetic energy term
Structure is undergoing a configurational change

 Step 2: Thermalization:
It thermalizes the configurations by heating up by stages until it reaches the target temperature.
Here, in “simulator.sh”:
E =
T =
-98.5290
0.00 K
Initial conformation
Energies are in Kcal/mol
Relaxed conformation
(from minimization step)
Thermalization conformations
1  5

 Step 3: MD  calculation of forces: using the velocityVerlet algorithm for integrating Newton’s equation of motion for each particle:
F i
 m i a i where F i
 
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V r i
, the force on particle i.
(Highly simplified description of MD)

 Step 4: Writing of the .pdb files:
At each desired time step, the new configuration is written in the
“min” files for each temperature.

The configurations are sorted by temperature.

 Allows a temporal correlation in the data, using autocorrelation analysis, to compute equilibrium averages.
 we can derive thermodynamical properties , including data from each temperature.

 How to use it:
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./ptwham_first
 will read data in each pXX/min file, calculate the
Rg, rmsd and end-to-end distance, and output files simXX.txt, wham_parameters.dat, beta.dat
edit wham_parameters.dat
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3) ./ptwham_second mintime maxtime
 writes “averages.txt” containing U (total energy), rmsd, Cv, end-to-end distance, writes
“free_energies.txt” containing Uk (average energy per replica), free energy and entropy and writes “deviations.txt” containing all the uncertainties on the above observables.

 The output:
Using 2 python scripts, we obtain the following plots:

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Calculates the rms distance between 2 configurations or between 1 configuration and a list of configurations taking into account their individual clusters for more accuracy.
Recognizes clusters from hydrogen bonds formed using the
DSSP definition of a hydrogen bond: the DSSP algorithm identifies a H-bond if E<-0.5 Kcal/mol.
 The program searches all the peptides forming H-bonds and rearranges the pdb file accounting for the chain order in the clusters formed.
How to use it: rmsd conf1.pdb list
It needs “ichain.dat”.

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The output files are : rmsd.txt  containing all the rmsd values for each configuration in the list id_order.txt
 containing all the clusters formed for each configuration in the list parallel_planes.txt
 containing a list of all the clusters being parallel to each other

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A python script that generates a graph showing acceptance probability for replica exchange.
Need “log.file” and “replicas.dat”

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Pymol scripts allowing to prepare the pdb files and make movies out of the configurations  unique_pymol command: unique_pymol file skip
Python scripts:
 extract_confs extracts a subset of configurations from a single file containing a list of configurations.
 repair_min repairs min files that are broken by a crash, removing all the incorrect lines.
Graphics scripts:
 trace_averages.py
( WHAM analysis ) command: ./trace_averages.py “averages.txt” “title” “1”
 trace_freeenergies.py
( WHAM analysis ) command: ./trace_freeenergies.py “free_energies.txt”
“title” “1”

You will find an updated version of the analysis tools on the wiki: http://riel.pmc.umontreal.ca/groups/biophysique/